Geologists working in offshore Brazil still vigorously debate the genetic origin of Cretaceous pre-salt lacustrine carbonates in the Santos Basin. Some carbonate petrologists have inferred that many of the macro-scale depositional features are of biological origin. Others contend that Brazilian pre-salt carbonate deposits are abiotic chemical precipitates formed in highly alkaline lakes. Each of these end-member paradigms has significant implications for how geologic models are constructed. To evaluate these genetic paradigms, detailed thin-section petrography (TSP), scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) were performed on thin sections and bulk core samples from well BM-S-22 Guarani-1ST (3-ESSO-004-SPS). The cored interval is characterized by a diverse boundstone assemblage including shrubs, spherulites, laminated sediments with abundant stevensite clay, domal and columnar stromatolites, oncoids, thrombolites, and travertine. In some boundstones, macro-scale structures and morphologies, such as crinkly-laminated stromatolites with centimeter-scale columnar relief, are highly suggestive of microbially-influenced sedimentation. SEM analyses of freshly broken core samples indicate that the columnar stromatolite/oncolite facies contains abundant evidence of fossilized microbes including microtubules, filaments, rods and molds that measure 1–2 μm in diameter and tens of μm in length. These features are similar in size and shape to modern and fossilized microbes. SEM observations coupled with geochemical evidence from within the various boundstone assemblages indicate that the influence of microbes on sedimentation within the Santos Basin is unequivocal. Although microscopic evidence does not illuminate the precise role microbes play within the basin (e.g., binding, trapping, baffling, or biostabilizing sediments) fossilized microbial features within the pre-salt suggest that depositional and reservoir models should account for their potential impact.